The constant evolution of analytical instrumentation consists in achieving faster data acquisition and improved instrument sensitivity. In the field of mass spectrometry, structural elucidation of ionized molecules is often carried out using a tandem mass spectrometer, where a particular precursor ion is selected at the first stage of analysis or in the first mass analyzer (MS-1), the precursor ions are subjected to fragmentation (e.g. in a collision cell), and the resulting fragment (product) ions are transported for analysis in the second stage or second mass analyzer (MS-2). The method can be extended to provide fragmentation of a selected fragment, and so on, with analysis of the resulting fragments for each generation. This is typically referred to an MSn spectrometry, with n indicating the number of steps of mass analysis and the number of generations of ions. Accordingly, MS2 corresponds to two stages of mass analysis with two generation of ions analyzed (precursor and products). As but one non-limiting example, tandem mass spectrometry is frequently employed to determine peptide amino acid sequences in biological samples. This information can then be used to identify peptides and proteins.
FIGS. 1A, 1B, 1C, 1D, 1E and 1F depict the components of a conventional mass spectrometer system 1. It will be understood that certain features and configurations of the mass spectrometer system 1 are presented by way of illustrative examples, and should not be construed as limiting the implementation of the present teachings in or to a specific environment. An ion source, which may take the form of an electrospray ion source 5, generates ions from an analyte material, for example the eluate from a liquid chromatograph (not depicted). The ions are transported from ion source chamber 10, which for an electrospray source will typically be held at or near atmospheric pressure, through several intermediate chambers 20, 25 and 30 of successively lower pressure, to a vacuum chamber 35 in which quadrupole mass filter (QMF) 51, an ion reaction cell 52 (such as a collision or fragmentation cell) and a mass analyzer 40 reside. Efficient transport of ions from ion source 5 to the vacuum chamber 35 is facilitated by a number of ion optic components, including quadrupole radio-frequency (RF) ion guides 45 and 50, octopole RF ion guide 55, skimmer 60, and electrostatic lenses 65 and 70. Ions may be transported between ion source chamber 10 and first intermediate chamber 20 through an ion transfer tube 75 that is heated to evaporate residual solvent and break up solvent-analyte clusters. Intermediate chambers 20, 25 and 30 and vacuum chamber 35 are evacuated by a suitable arrangement of pumps to maintain the pressures therein at the desired values. In one example, intermediate chamber 20 communicates with a port of a mechanical pump (not depicted), and intermediate pressure chambers 25 and 30 and vacuum chamber 35 communicate with corresponding ports of a multistage, multiport turbomolecular pump (also not depicted).
Electrodes 80 and 85 (which may take the form of conventional plate lenses) positioned axially outward from the mass analyzer 40 in the generation of a potential well for axial confinement of ions, and also to effect controlled gating of ions into the interior volume of the mass analyzer 40. The mass analyzer 40 is additionally provided with at least one detector that generates a signal representative of the abundance of ions that exit the mass analyzer, generally after been selected in the mass analyzer according to their mass-to-charge (m/z) ratio. If the mass analyzer 40 is provided as a quadrupole mass filter, then a detector at detector position 54 will generally be employed so as to receive and detect those ions which selectively completely pass through the mass analyzer 40 from an entrance end to an exit end. If alternatively, the mass analyzer 40 is provided as a linear ion trap that performs mass analysis by selective ejection of ions, then one or more detectors at detector positions 90 may be employed.
Ions enter an inlet end of the mass analyzer 40 as a continuous or quasi-continuous beam after first passing, in the illustrated conventional apparatus, through a quadrupole mass filter (QMF) 51 and an ion reaction cell 52. The QMF 51 may take the form of a conventional multipole structure operable to selectively transmit ions within an m/z range determined by the applied RF and DC voltages. The collision cell 52 may also be constructed as a conventional multipole structure to which an RF voltage is applied to provide radial confinement. The interior of the collision cell 52 is pressurized with a suitable collision gas, and the kinetic energies of ions entering the collision cell 52 may be regulated by adjusting DC offset voltages applied to QMF 51, collision cell 52 and tens 53.
The mass spectrometer system 1 shown in FIG. 1A may operate as a conventional triple quadrupole mass spectrometer, wherein ions are selectively transmitted by QMF 51, fragmented in the ion reaction cell 52, and wherein the resultant product ions are mass analyzed so as to generate a product-ion mass spectrum by mass analyzer 40 and one of the detectors 54, 90. Samples may be analyzed using standard techniques employed in triple quadrupole mass spectrometry, such as precursor ion scanning, product ion scanning, single- or multiple reaction monitoring, and neutral loss monitoring, by applying (either in a fixed or temporally scanned manner) appropriately tuned RF and DC voltages to QMF 51 and mass analyzer 40. The operation of the various components of the mass spectrometer systems may be directed by a control and data system 44, which will typically consist of a combination of general-purpose and specialized processors, application-specific circuitry, and software and firmware instructions. The control and data system 44 may also provide data acquisition and post-acquisition data processing services.
FIG. 1B is a more-detailed depiction of the ion reaction cell 52 and showing the electrodes 53 and 80. As illustrated, the ion reaction cell comprises a multipole device specifically a quadrupole comprising four elongated and substantially parallel rod electrodes arranged as a pair of first rod electrodes 56 and a pair of second rod electrodes 46. The leftmost diagram of FIG. 1B provides a longitudinal view and the rightmost diagram provides a transverse cross-sectional view, respectively, of the ion reaction cell 52. Note that only one of the rod electrodes 46 is shown, since the view of the second rod electrode 46 is blocked. The four rod electrodes define an axis 59 of the device that is, parallel to the rod electrodes 46, 56 and that is centrally located between the rod electrodes; in other words, the four rod electrodes 46, 56 are equidistantly radially disposed about the axis 59. Although the reaction cell 53 is shown with four rods so as to generate a quadrupolar electric field, the reaction cell may alternatively comprise six (6) rods, eight (8) rods, or even more rods so as to generate a hexapotar, octopolar, or higher-order electric field respectively. The rod electrodes may be contained within a housing 57 which serves to contain a collision gas used for collision induced dissociation of precursor ions introduced into a trapping volume between the rod electrodes 46, 56 through an entrance end 58a. 
FIG. 1C schematically illustrates typical basic electrical connections for the rod electrodes 46, 56. RF modulated potentials provided by power supply 250 are applied to points A and B, which are electrically connected to electrodes 46 and electrodes 56, respectively. The electrode of each pair of electrodes—that is, the pair of electrodes 46 and the pair of electrodes 56—are diametrically opposed to one another with respect to the ion occupation volume longitudinal axis 59. The phase of the RF voltage applied to one of the pairs of electrodes is always exactly out of phase with the phase applied to the other pair of electrodes. Optionally, the power supply 250 may provide a DC offset potential such that point A is maintained at a first DC potential and such that point B is maintained at either the first DC potential or at a second DC potential. Accordingly, in some embodiments, a DC potential difference may exist between the first pair 56 and the second pair 46 of rod electrodes.
In known fashion, application of RF potentials to the rod electrodes 46, 56 as discussed above produces an electric field pseudo-potential well about and in close proximity to the central axis 59. In operation, ion lenses or electrodes, such as entrance electrode 53 and others (not shown) are used to propel ions into the entrance end 58a (FIG. 1B) of the multipolar rod set (e.g., rod electrodes 46, 56) defined by a set of first ends of the plurality of rods. The presence of the pseudo-potential well causes the ions to remain in an ion trapping volume in the vicinity of the axis 59 as these ions progress through the reaction cell from the entrance end 58a to an exit end 58b of the multipolar rod set.
The ion trapping volume does not have sharp boundaries that can be precisely located. In any event, however, the true trapping volume lies within the region 12 denoted by lines connecting the innermost points of the four rod electrodes. Thus the region 12 can be considered to comprise a practical trapping volume that is defined by the electrodes themselves such that the true trapping volume resides within the practical trapping volume 12. Both the practical trapping volume and the true trapping volume are elongated parallel to the axis 59 between the entrance end 58a and the exit end 58b. The entrance and exit ends 58a, 58b are defined by the ends of the rod electrodes 46, 56. The ion trapping produced by the application of the RF field is effective in directions that are radial to the axis 59 (that, is within transverse cross-sectional planes such as the one illustrated on the right-hand side of FIG. 1B). In most conventional operation of collision or reaction cells, the ions are not trapped parallel to or along the axis 59.
Although the reaction cell 52 shown in FIG. 1B is illustrated with straight, parallel rod electrodes, alternative reaction cell configurations are known in which the electrodes are curved. For example, the reaction cell 62 shown in FIG. 1D comprises a pair of first elongated electrodes 66 and a pair of second elongated electrodes 76, each of which comprises an arc segment such as a segment of a circular ring. Only one of the electrodes 76 is illustrated, since the second such electrode is behind the illustrated electrode 76 and therefore hidden from view. Alternatively, six, eight or some other number of electrodes could be employed. Alternatively, the curved elongated electrodes need not be in the form of circular arcs and may be formed, for example, with elliptical or parabolic curvature.
In operation, radio frequency (RF) and optional DC voltages are applied to the electrodes 66 and 76 as previously described (see FIG. 1B) and, consequently, ions propagating through the device 62, after introduction into the device at entrance end 68a, tend to follow the path of a curved axis 59 through the device from the entrance end 68a to an exit end 68b, with the axis 59 being defined centrally with respect to the set of curved electrodes. For the illustrated reaction cell 62, the curved central axis may be considered to be co-extensive with an arc of a circular section having a radius of curvature. The curved reaction cell provides an elongate ion trapping volume that closely follows the curved axis 59 between the entrance end 68a and the exit end 68b. Similarly an elongate operational trapping volume that contains the true trapping volume may be defined with reference to the curved rod electrodes 66 and 76 in a fashion similar to that described previously.
Curved reaction cells such as the reaction cell 62 shown in FIG. 1D enable the folding or turning of ion paths and allow smaller “footprints” than would otherwise be required for straight reaction cells (e.g., FIG. 1B). However, they are associated with a potential disadvantage in that ions having high kinetic energy may fly out of the vicinity of the curved axis and consequently develop unstable trajectories which will cause them to be ejected from the device or else contact the electrodes. As one means to address this issue, U.S Patent Application Pre-Grant Publication No. 2009/0095898 A1, in the names of inventors Collings et al., describes collision cells that include both curved sections and straight sections, the straight sections being of lengths selected in order to allow precursor ions to lose enough kinetic energy, as they pass through the straight sections, to allow the precursor ions to travel through the curved sections without either escaping the collision cell or colliding with the collision cell electrodes. Alternatively, U.S Patent Application Pre-Grant Publication No. 2010/0301227 A1, in the name of inventor Muntean, describes ion guides, including collision cells, having ion deflecting devices that are configured for applying a radial DC electric field across the ion guide region at a magnitude that varies along the curved central axis.
In some instances, the elevated collision gas pressure within a collision cell can cause product ions that have been formed in the collision cell to drain out of the cell slowly or possibly even stall within the collision cell as a result of their very low velocity after many collisions with neutral gas molecules. The resulting lengthened ion clear-out time can cause interference between adjacent channels when several ion pairs (i.e., parent/products) are being measured in rapid succession. U.S. Pat. No. 5,847,386, in the names of inventors Thomson et al., describes several apparatus configurations that are designed to reduce this problem through the provision of an electric field that is parallel to the device axis within the space between the elongated electrodes. For example, the aforementioned patent teaches that this axial field can be created by tapering the rods, or arranging the rods at angles with respect to each other. In one apparatus example that includes elongated rod electrodes that are tapered along their length, the rods of one pair (e.g., either rods 46 or 56 as shown in FIG. 1B) is oriented so that the wide ends of the rods are at the entrance end 58a and the narrow ends are at the exit end 58b of the rod set and the other pair is oriented so that its wide ends are at the exit end 58b and so that its narrow ends are at the entrance end 58a. The provision of a first DC offset voltage on one of the tapered rod pairs and a second DC offset voltage on the other tapered rod pair (see FIG. 1C) then causes the axial field to be formed within the interior volume between the rods.
Another apparatus configuration described in the aforementioned U.S. Pat. No. 5,847,386 includes segmented rods, wherein different DC offset voltages are applied to each respective segment such that ions within the interior volume experience a stepped DC electrical potential in a direction from the entrance end to the exit end. For example, FIG. 1E illustrates a collision cell or reaction cell 152 in which the rods 46 and the rods 56 (as shown in and previously described in reference to FIG. 1B) are replaced by series of rod segments 146 and 156, respectively. Each segment 146 is supplied with the same RF voltage and each segment 156 is supplied with the same phase-shifted RF voltage from power supply 250 via a set of isolating capacitors (not illustrated), but each is supplied with a different DC voltage.
U.S. Pat. No. 7,675,031, in the names of inventors Konicek et al. and assigned to the assignee of the present invention, describes an alternative apparatus configuration to address the problem of slowed ion movement through a collision cell. This latter patent teaches the use of auxiliary electrodes for creating drag fields within the cell interior volume. The auxiliary electrodes may be provided as arrays of finger electrodes for insertion between main RF electrodes (e.g., the rod electrodes 46, 56 shown in FIG. 1B or the rod electrodes 66, 76 shown in FIG. 1D) of a multipole device. The finger electrodes may be provided on thin substrate material such as printed circuit board material. A progressive range of voltages can be applied along lengths of the auxiliary electrodes by implementing a voltage divider that utilizes static resisters interconnecting individual finger electrodes of the arrays. Dynamic voltage variations may be applied to individual finger electrodes or to groups of the linger electrodes.
FIG. 1F shows a simplified depiction of one exemplary configuration taught in U.S. Pat. No. 7,675,031. The leftmost view of FIG. 1F is a longitudinal view of the apparatus 252 showing, very schematically, the disposition of auxiliary electrodes 77, which may be configured with one or more terminal finger electrodes, between the main rod electrodes 46, 56, wherein these rod electrodes are as shown in FIG. 1B. The rightmost view of FIG. 1F is a transverse cross-sectional view which more accurately show how the auxiliary electrodes 77 are disposed between adjacent pairs of the main rod electrodes. The auxiliary electrodes can occupy positions that generally define planes that, if extended, intersect on the central axis 59. These planes can be positioned between adjacent RF rod electrodes at about equal distances from the main RF electrodes of the multipole ion guide device where the quadrupolar fields are substantially zero or close to zero, for example. Thus, the configured arrays of finger electrodes 71 can lie generally in these planes of zero potential or close to zero potential so as to minimize interference with the quadrupolar fields. The array of auxiliary electrodes and finger electrodes can also be adapted for use with curved quadrupolar configurations such as the configuration shown in FIG. 1D.
Mass spectrometers which utilize the measurements of ion current (triple quadrupole mass spectrometers for example) have a sensitivity limit defined by the minimum current which the mass spectrometer detector can dependably distinguish from background signal and random “noise”. This fact limits the lowest analyte abundance which can be reliably detected in such systems. Although mass spectrometers that measure induced image currents (such as Fourier-Transform Ion Cyclotron Resonance and orbital trap mass spectrometers) offer greater sensitivity, the ion-current-detecting types of systems are in widespread use. Unfortunately, many diagnostic analyte compounds are present at low concentrations in natural samples. This problem may be exacerbated during tandem mass spectrometry measurements since any particular precursor ion type will generally give rise to a variety of product ion types and, thus, any product ion type will be present at a lower abundance than that of the precursor ion from which it was generated. Moreover, some quantity of ions is invariably lost during each of the various ion manipulation steps associated with tandem mass spectra measurements. These factors significantly limits the application of the aforementioned ion-current-detecting instruments applications in which analytes of interest are present at low and therefore potentially undetectable concentrations. Thus, there is a need in the art for methods and systems that can enable such systems to make reliable detection and quantification measurements of low-abundance product ions generated in tandem mass spectrometry.